Contacts of the helix formed by residues 2798 - 2819 (chain H) in PDB entry 6X34
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER2798 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2796H THR 3.9 1.4 + - - -
2797H PHE* 1.3 77.7 - - - +
2799H GLU* 1.3 61.8 + - - +
2800H LYS* 3.3 7.2 - - - -
2801H ASP* 3.9 10.5 - - - +
2802H LYS* 3.0 27.4 + - - +
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Residues in contact with GLU2799 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2798H SER* 1.3 77.0 - - - +
2800H LYS* 1.3 62.3 + - - +
2802H LYS* 4.0 4.9 - - - +
2803H GLU* 3.2 24.1 + - - +
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Residues in contact with LYS2800 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2798H SER* 3.3 4.8 - - - -
2799H GLU* 1.3 78.3 - - - +
2801H ASP* 1.3 63.0 + - - +
2803H GLU* 3.5 12.9 + - - +
2804H ILE* 3.8 8.8 + - - +
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Residues in contact with ASP2801 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2797H PHE* 3.8 23.6 - - + -
2798H SER* 3.5 11.1 + - - +
2799H GLU 3.4 0.2 - - - -
2800H LYS* 1.3 79.3 - - - +
2802H LYS* 1.3 62.1 + - - +
2804H ILE* 3.4 18.3 + - - +
2805H TYR* 4.4 2.8 + - - +
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Residues in contact with LYS2802 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2759H ALA* 4.9 5.3 - - + +
2794H TYR 5.7 2.5 - - - +
2797H PHE* 4.4 8.7 - - + +
2798H SER 3.0 18.8 + - - +
2799H GLU* 4.1 5.2 - - - +
2801H ASP* 1.3 76.7 - - - +
2803H GLU* 1.3 58.3 + - - +
2804H ILE 3.2 0.4 + - - -
2805H TYR* 3.5 4.8 + - - +
2806H ARG* 3.2 27.3 + - + +
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Residues in contact with GLU2803 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2799H GLU 3.2 18.0 + - - +
2800H LYS* 3.8 9.0 - - - +
2801H ASP 3.3 0.8 - - - -
2802H LYS* 1.3 74.6 - - - +
2804H ILE* 1.3 62.6 + - - +
2805H TYR 3.3 0.2 - - - -
2806H ARG* 3.8 9.2 - - - -
2807H TRP* 3.2 26.0 + - - +
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Residues in contact with ILE2804 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2800H LYS 3.8 7.3 + - - +
2801H ASP* 3.4 13.6 + - - +
2802H LYS 3.2 1.2 - - - -
2803H GLU* 1.3 80.7 - - - +
2805H TYR* 1.3 59.2 + - - +
2807H TRP* 4.2 8.1 + - - +
2808H PRO* 4.6 5.4 - - - +
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Residues in contact with TYR2805 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2759H ALA* 4.1 31.7 - - + +
2762H THR* 5.1 9.2 - - - -
2763H HIS* 5.2 7.9 - - + +
2801H ASP 4.4 2.4 + - - +
2802H LYS* 3.5 5.3 + - - +
2804H ILE* 1.3 77.5 - - - +
2806H ARG* 1.3 62.7 + - - +
2807H TRP 3.3 1.2 + - - -
2808H PRO* 3.8 12.1 - - - +
2809H ILE* 3.8 11.1 + - - +
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Residues in contact with ARG2806 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2755H ILE* 5.3 10.9 - - + +
2759H ALA* 4.3 11.9 - - + +
2802H LYS* 3.2 19.6 + - + +
2803H GLU* 4.2 6.7 - - - -
2804H ILE 3.5 0.2 - - - -
2805H TYR* 1.3 76.8 - - - +
2807H TRP* 1.3 59.7 + - - +
2809H ILE* 3.5 5.9 + - - +
2810H LYS* 3.0 31.6 + - - +
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Residues in contact with TRP2807 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2803H GLU 3.2 19.2 + - - +
2804H ILE* 4.3 5.8 - - - +
2805H TYR 3.3 0.4 - - - -
2806H ARG* 1.3 77.2 - - - +
2808H PRO* 1.3 58.0 - - - +
2810H LYS* 4.0 4.0 - - - +
2811H GLU* 3.0 30.7 + - - +
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Residues in contact with PRO2808 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2804H ILE 4.6 4.1 - - - +
2805H TYR* 3.8 11.0 - - - +
2806H ARG 3.3 0.2 - - - -
2807H TRP* 1.3 79.5 - - - +
2809H ILE* 1.3 60.3 + - - +
2811H GLU* 3.7 5.4 + - + +
2812H SER* 3.3 22.9 + - - -
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Residues in contact with ILE2809 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2755H ILE* 4.9 16.2 - - + +
2758H PHE* 4.7 19.5 - - + -
2759H ALA 5.5 1.8 - - - +
2805H TYR 3.8 10.1 + - - +
2806H ARG* 3.5 8.6 + - - +
2807H TRP 3.4 0.6 - - - -
2808H PRO* 1.3 76.1 - - - +
2810H LYS* 1.3 60.4 + - - +
2812H SER* 3.5 5.3 + - - -
2813H LEU* 3.0 28.6 + - - +
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Residues in contact with LYS2810 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2755H ILE* 5.9 5.3 - - + +
2806H ARG 3.0 19.1 + - - +
2807H TRP* 4.0 4.9 - - - +
2809H ILE* 1.3 75.6 - - - +
2811H GLU* 1.3 59.1 + - - +
2813H LEU* 3.8 4.7 - - - +
2814H LYS* 2.9 31.5 + - - +
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Residues in contact with GLU2811 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2742H THR* 4.8 8.3 - - - -
2807H TRP 3.0 19.2 + - - +
2808H PRO* 4.0 5.6 - - + +
2810H LYS* 1.3 76.9 - - - +
2812H SER* 1.3 60.2 + - - +
2814H LYS* 3.6 5.7 + - - +
2815H ALA* 3.2 23.0 + - - +
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Residues in contact with SER2812 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2808H PRO 3.3 15.5 + - - -
2809H ILE* 3.9 5.4 - - - -
2810H LYS 3.3 0.2 - - - -
2811H GLU* 1.3 78.1 - - - +
2813H LEU* 1.3 63.1 + - - +
2815H ALA* 3.5 6.8 + - - +
2816H MET* 3.4 19.9 + - - +
2878H LEU* 6.3 2.9 - - - -
2926H LEU* 5.4 12.3 - - - -
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Residues in contact with LEU2813 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2751H LEU* 6.3 3.4 - - + -
2809H ILE 3.0 18.8 + - - +
2810H LYS* 3.9 6.1 - - - +
2812H SER* 1.3 76.8 - - - +
2814H LYS* 1.3 63.5 + - - +
2816H MET* 3.4 6.4 + - - +
2817H ILE* 3.2 21.3 + - - +
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Residues in contact with LYS2814 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2742H THR* 3.8 23.0 - - - +
2745H VAL* 3.8 30.7 - - + +
2810H LYS 2.9 17.9 + - - +
2811H GLU* 4.0 1.8 - - - +
2812H SER 3.3 0.2 - - - -
2813H LEU* 1.3 75.3 - - - +
2815H ALA* 1.3 64.4 + - - +
2817H ILE* 3.4 6.1 + - - +
2818H ALA* 3.3 19.9 + - - +
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Residues in contact with ALA2815 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2740H VAL* 4.8 18.2 - - + +
2741H GLU 6.0 0.4 - - - -
2742H THR* 4.8 5.8 - - - -
2811H GLU 3.2 16.6 + - - +
2812H SER* 3.8 7.0 - - - +
2813H LEU 3.3 0.6 - - - -
2814H LYS* 1.3 78.2 - - - +
2816H MET* 1.3 61.2 + - - +
2818H ALA* 3.4 15.0 + - - +
2819H TRP* 3.5 11.4 + - - +
2881H ASN* 5.2 13.7 - - + -
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Residues in contact with MET2816 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2812H SER 3.4 10.7 + - - +
2813H LEU* 3.8 8.7 - - - +
2814H LYS 3.3 0.6 - - - -
2815H ALA* 1.3 76.3 - - - +
2817H ILE* 1.3 64.9 + - - +
2819H TRP* 3.3 13.7 + - - +
2821H TRP* 3.3 32.5 + - + +
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Residues in contact with ILE2817 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2745H VAL* 5.2 6.5 - - + -
2746H ILE 5.3 8.1 - - - +
2813H LEU 3.2 15.9 + - - +
2814H LYS* 3.7 9.0 - - - +
2815H ALA 3.3 0.4 - - - -
2816H MET* 1.3 77.5 - - - +
2818H ALA* 1.3 60.5 + - - +
2820H GLU* 3.4 12.8 + - - -
2821H TRP 5.0 6.7 - - - +
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Residues in contact with ALA2818 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2740H VAL* 5.2 8.7 - - + -
2741H GLU 4.5 15.7 - - - +
2745H VAL* 5.7 2.8 - - + +
2814H LYS 3.3 10.7 + - - +
2815H ALA* 3.8 10.5 - - - +
2816H MET 3.3 0.6 - - - -
2817H ILE* 1.3 77.7 - - - +
2819H TRP* 1.3 56.7 + - - +
2820H GLU* 3.2 5.5 + - - +
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Residues in contact with TRP2819 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2815H ALA 3.5 9.0 + - - +
2816H MET* 3.3 11.8 + - - +
2817H ILE 3.2 1.4 - - - -
2818H ALA* 1.3 76.2 - - - +
2820H GLU* 1.3 69.9 + - - +
2821H TRP* 3.3 5.1 + - + +
2939H ARG* 5.4 4.5 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il